Re: Graphene pdb/psf files cannot be read by psfgen

From: Wanzhi Qiu (wanzhiqiu128_at_yahoo.com)
Date: Wed Feb 15 2012 - 22:41:23 CST

Hi Subbarao, Thanks very much for sharing your knowledge. I'll have a look at the nanotube tutorial and try your ideas. Kind regards, wanzhi ________________________________ From: kanchi subbarao rao <ksubbu85_at_gmail.com> To: Wanzhi Qiu <wanzhiqiu128_at_yahoo.com> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> Sent: Thursday, 16 February 2012 2:48 PM Subject: Re: namd-l: Graphene pdb/psf files cannot be read by psfgen Hi wanzhi,     In my procedure every thing is fine. I thought that You wrote correct .psf for Graphene.Any way I am telling what I did. First do the tutorial for Carbon nanotube , which is given in NAMD tutorials.IN that there is a tcl scripting for creating .psf for cnt. by using that I Created .psf for graphene. For that I wrote A topology (for Bonding ) file and .pgn file  for graphene by using .pdb file which is generated in VMD.By using this trick I did. I think now you may do better. cheers subbarao kanchi physics Dept IISC Bangalore INDIA          On Thu, Feb 16, 2012 at 7:42 AM, Wanzhi Qiu <wanzhiqiu128_at_yahoo.com> wrote: Hi Subbarao, > > >Thank you! In my situation the first step outlined in your procedure fails - the merge cannot be done due to failure in reading psf/pdb files. I guess something is wrong with my graphene pdf/pdb files generated using VMD's Carbon Nanostructure Builder. Could you let me know which tool you used to generate your graphene pdb/psf files. > > >Many thanks, > > >wanzhi > > > > > >________________________________ > From: kanchi subbarao rao <ksubbu85_at_gmail.com> >To: Cruz-Chu Eduardo Roberto <eduardo.cruz_at_mavt.ethz.ch> >Cc: Wanzhi Qiu <wanzhiqiu128_at_yahoo.com>; "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> >Sent: Thursday, 16 February 2012 1:11 AM > >Subject: Re: namd-l: Graphene pdb/psf files cannot be read by psfgen > > >hi  Wanzhi, > >I also faced the same problem.I created .psf and .pdb files for graphene.But when we added to some other system by using merge structures in VMD some coordinates become zero's.The solution which I find for this as follows > >1.  After merging the the two structure in VMD I got .psf and .pdb files. >2. I added the two coordinate files with VMD ( manually in the same order as you gave in merge structures ) >3. loaded the .psf file witch you built in VMD (merge structures) and manually added .pdb  in VMD >4.By using save coordinates was gave correct .pdb file for combined structure. > > >I Hope It will work for you.But If you find any other solution,Let me know > >cheers > >subbarao kanchi >physics Dept >IISC Bangalore >INDIA   > > > >On Wed, Feb 15, 2012 at 4:36 PM, Cruz-Chu Eduardo Roberto <eduardo.cruz_at_mavt.ethz.ch> wrote: > >readpsf command must go before coordpdb; that is: >> >>readpsf graphene.psf >> >>coordpdb graphene.pdb >> >> >>then you add other molecules >> >>readpsf smth.psf >>coordpdb smth.pdb >> >>and output the final structure >> >>writepsf final.psf >>writepdb final.pdb >> >>a more detailed explanation is provided in the psfgen user guide, available in the website. >> >> >>Regards; >> >>Eduardo >> >>On Feb 15, 2012, at 8:14 AM, Wanzhi Qiu wrote: >> >>Dear NAMDers, >> >>I constructed a small graphene sheet using VMD Carbon Nanostructure Builder with options of Bonds, Angles etc are ticked. The result is shown on VMD OpenGL window and pdb/psf files are then generated using writepdb/writepsf commands in Tk console. The files appear to be correct with numbers for bonds, angles etc in the psf file. However, they fail when I try to combine the graphene with other molecules. >> >>The problem is that the generated  graphene.pdb/graphene.psf cannot be read by psfgen. In particular, the commands issued in the Tk console and error messages are: >> >>>coordpdb graphene.pdb >>gives following result: >> >>psfgen) reading coordinates from pdb file graphene.pdb >>psfgen) no segment >>psfgen) Warning: failed to set coordinate for atom C     GRA:1 >>(patten repeat for all atoms) >> >>>readpsf graphene.psf >>gives following result: >> >>psfgen) reading structure from psf file graphene.psf >>psfgen) error reading atoms >>MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over. >> >>I suspect that the problem might be related to the residue name "GRA" in the pdb file. The first 3 lines of the pdb file are: >> >>CRYST1    8.508    7.368  100.000  90.00  90.00  90.00 P 1           1 >>ATOM      1  C   GRA X   1       0.000   0.000   0.000  0.00  0.00           C >>ATOM      2  C   GRA X   2      -0.709   1.228   0.000  0.00  0.00           C >> >>Please let me know if you have any advices/comments/suggestions. >> >>Many thanks, >> >>Wanzhi >> >>----------- >>Wanzhi Qiu, Ph. D. >>Senior Researcher >>National ICT Australia >>Department of Electrical & Electronic Engineering >>The University of Melbourne Parkville, Victoria 3010 Australia >> >> >> >> > > >

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